KO assignment questions

[Elizabeth Trembath-Reichert]

I saw this note: "With the exception of KEGG Orthology, all other assignments are done using hmmsearch from HMMER 3.1b2 package, with model-specific trusted cutoff for Pfam, noise cutoff for TIGRFAM or with --domE 0.01 cutoff for the rest of the families. KEGG Orthology Terms are assigned using lastal 983 against KEGG Genes v77.1 to assign KO Terms to IMG-NR genes, which is then used to assign KO Terms to the rest of the genes. IMG-NR version used for annotation is reported in dataset-specific 'sigs_anntoation_parameters' file."

And was wondering why lastal was used instead of hmm (as would be for programs like kofam) for KO assignment? 

Also, is there any contig size exclusion (like all contigs below 1kb removed) before functional annotation in IMG annotation pipelines?

Thank you!

Elizabeth

[Rekha Seshadri]

Hi Elizabeth - short answer is that KO does not comprise HMM models or profiles.

As for minimum contig length - it is 200 bp in general, 500 for combined assemblies or JGI metagenome standard draft products.

See metagenome annotation pipeline publication for other details.

[Rekha Seshadri]

Further clarification - we have not implemented KOfam which is relatively recent.